Package Recipe 'bioconductor-tvtb'

recipe bioconductor-tvtb

TVTB: The VCF Tool Box

Homepage: https://bioconductor.org/packages/3.13/bioc/html/TVTB.html
License: Artistic-2.0
Recipe: /bioconductor-tvtb/meta.yaml
Links: biotools: tvtb, doi: 10.1038/nmeth.3252

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

package bioconductor-tvtb¶

Versions

1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.8.0-0, 1.6.0-0, 1.4.0-0

Depends

bioconductor-annotationfilter >=1.16.0,<1.17.0
bioconductor-biocgenerics >=0.38.0,<0.39.0
bioconductor-biocparallel >=1.26.0,<1.27.0
bioconductor-biostrings >=2.60.0,<2.61.0
bioconductor-ensembldb >=2.16.0,<2.17.0
bioconductor-ensemblvep >=1.34.0,<1.35.0
bioconductor-genomeinfodb >=1.28.0,<1.29.0
bioconductor-genomicranges >=1.44.0,<1.45.0
bioconductor-gviz >=1.36.0,<1.37.0
bioconductor-iranges >=2.26.0,<2.27.0
bioconductor-limma >=3.48.0,<3.49.0
bioconductor-rsamtools >=2.8.0,<2.9.0
bioconductor-s4vectors >=0.30.0,<0.31.0
bioconductor-summarizedexperiment >=1.22.0,<1.23.0
bioconductor-variantannotation >=1.38.0,<1.39.0
r-base >=4.1,<4.2.0a0
r-ggally
r-ggplot2
r-reshape2

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-tvtb

and update with:

conda update bioconductor-tvtb

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-tvtb:<tag>

(see bioconductor-tvtb/tags for valid values for <tag>)

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tvtb/README.html)